Vault Hooks into both CraftConomy and Essentials, and this means that i get two different balances, depending on if i use /balance (Essentials) or /money (craftconomy) if i spend money with they are withdrawn from essentials economy and not in craftconomy as intended?

depends on priority of the registrations. Whichever has a higher priority will get utilized. In general, don't use Essentials Economy if you want to use a different one.